Package: occumb 1.1.0.9008

occumb: Site Occupancy Modeling for Environmental DNA Metabarcoding

Fits multispecies site occupancy models to environmental DNA metabarcoding data collected using spatially-replicated survey design. Model fitting results can be used to evaluate and compare the effectiveness of species detection to find an efficient survey design. Reference: Fukaya et al. (2022) <doi:10.1111/2041-210X.13732>.

Authors:Keiichi Fukaya [aut, cre], Ken Kellner [cph], Mika Takahashi [aut]

occumb_1.1.0.9008.tar.gz
occumb_1.1.0.9008.zip(r-4.5)occumb_1.1.0.9008.zip(r-4.4)occumb_1.1.0.9008.zip(r-4.3)
occumb_1.1.0.9008.tgz(r-4.4-any)occumb_1.1.0.9008.tgz(r-4.3-any)
occumb_1.1.0.9008.tar.gz(r-4.5-noble)occumb_1.1.0.9008.tar.gz(r-4.4-noble)
occumb_1.1.0.9008.tgz(r-4.4-emscripten)occumb_1.1.0.9008.tgz(r-4.3-emscripten)
occumb.pdf |occumb.html✨
occumb/json (API)
NEWS

# Install 'occumb' in R:
install.packages('occumb', repos = c('https://fukayak.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/fukayak/occumb/issues

Uses libs:
  • jags– Just Another Gibbs Sampler for Bayesian MCMC
  • c++– GNU Standard C++ Library v3
Datasets:
  • fish - Fish eDNA metabarcoding dataset
  • fish_raw - Fish eDNA metabarcoding dataset

On CRAN:

5.11 score 8 scripts 222 downloads 12 exports 12 dependencies

Last updated 18 days agofrom:8f88508e5d. Checks:OK: 1 NOTE: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 05 2024
R-4.5-winNOTENov 05 2024
R-4.5-linuxNOTENov 05 2024
R-4.4-winNOTENov 05 2024
R-4.4-macNOTENov 05 2024
R-4.3-winNOTENov 05 2024
R-4.3-macNOTENov 05 2024

Exports:eval_util_Leval_util_Rget_post_samplesget_post_summarygoflist_cond_Llist_cond_RoccumboccumbDataplotpredictsummary

Dependencies:backportscheckmatecodacrayonevaluatehighrjagsUIknitrlatticerjagsxfunyaml

Introduction to occumb

Rendered fromoccumb.Rmdusingknitr::rmarkdownon Nov 05 2024.

Last update: 2024-11-05
Started: 2023-07-20

Model specification in occumb()

Rendered frommodel_specification.Rmdusingknitr::rmarkdownon Nov 05 2024.

Last update: 2024-03-08
Started: 2023-07-20